Download Background: In Unique Nucleotide Sequence (UNS)

Background:
In Unique Nucleotide Sequence (UNS)-guided assembly, homology sequences have
been standardized (e.g. U1, U2, U3…UX) and have been computationally optimized for
proper assembly (reduction of hairpins, sequence homology, and GC tracts) and ease of
use (no start codons or useful restriction site)1,2. Genetic cassettes that are to be
connected are cloned into Part Vectors, which contain the UNSes that surround the
insert. Restriction enzymes are used to digest Part Fragments out of the Part Vectors;
these fragments can be Gibson assembled into a Linearized Destination Vector that
contains the Gibson homology sequence (U1) and the final (UX). This assembly strategy
has been adapted to build recombinase-based Boolean logic and arithmetic circuits in
mammalian cells3. Relevant plasmid maps and sequences from this work are found
here: link.
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Part Entry Vectors:
We’ve included eight Part Entry Vectors, which contain an MluI/Acc65I cloning region
where gene cassettes are to be inserted and replace a small 8bp sequence that
separates the restriction sites. The cloning region is surrounded by UNSes. For Part
Entry Vector N, the cloning sequence is surrounded by a UN sequence to the left and to
the right, UN+1 and Ux. These vectors contain promoter and terminator sequences.
Though these are extraneous sequences and are not needed for the UNS assembly,
they can be used to test for expression of genes contained in the Part Vectors.
Part Entry Vectors:
 PV1-PV4: pBW701, 702, 703, 704 (Addgene: 87561, 87562, 87563, 87564)
 PV5-PV8: pBW751, 752, 753, 754 (Addgene: 87565, 87566, 87567, 87568)
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Part Vectors:
We’ve included some completed Part Vectors which contain inserted genetic sequences
that relate to building BLADE recombinase-based circuits. Here is an example of the four
Part Vectors to assemble the 2-input decoder circuit. Recombinase sites are placed after
the MluI restriction site and prior to an introduced AgeI restriction site. Fluorescent
protein sequences follow this along with bovine growth hormone polyA sequences.
BLADE-associated Part Vectors:
 2-input-4-output BLADE decoder:
o pBW768, 759, 769, 770 (Addgene: 87574, 87575, 87576, 87577)

2-input-2-output BLADE library:
o pBW705, 706, 707, 708 (Addgene: 87569, 87570, 87571, 87572)

3-input-2-output BLADE full adder:
o pBW758, 759, 806, 807, 808, 809, 810, 811
(Addgene: 87580, 87575, 87582, 87583, 87584, 87585, 87586, 87587)

2-input BLADE guide RNA system*:
o pBW1720, 1942, 1943, 1944 (Addgene: 89053, 89055, 89056, 89057)
*guide RNA sequences can be entered into these plasmids using an oligo annealing/ligation much like as
found here with x330 series plasmids: link.
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Part Fragments:
The AscI, NotI, and NheI enzymes can be used to digest out cassettes with UNS
overhangs included. The first set of Part Vectors are digested with AscI and NotI to
reveal the UN and UN+1 sequences, whereas, the final Part Vector is digested with AscI
and NheI to reveal the UN and UX sequences. Fragments can be isolated via gel
extraction.
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Destination Vector:
Destination Vectors contain U1 and UX UNSes, where Part Fragments will be assembled
into via Gibson isothermal assembly. To expose the U1 and UX, a NotI and EcoRI
digestion can be performed and the backbone can be isolated by PCR cleanup (as the
sequence between the U1 and UX sites is very short (8bp) and will run through the
column).
Destination Vectors:
 Constitutive RNApol II expression by pCAG (U1-UX): pBW700 (Addgene: 87578)
 Constitutive RNApol II expression by pCAG (U5-UX)*: pBW755 (Addgene: 89507)
 Constitutive RNApol III expression by hU6 (U1-UX): pBW1716 (Addgene: 87579)
* This Destination Vector can be used to assembly Part Fragments beginning with U5 rather than U1 and
can be used to break up larger multi-piece assemblies.
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Gibson Assembly to Create Final Expression Vector:
Part Fragments and a Linearized Destination Vector can be combined in a Gibson
isothermal assembly reaction2 to produce the final Expression Vector.
Expression Vectors:
 2-input-4-output BLADE fluor. protein decoder: pBW842 (Addgene: 87551)
 3-input-2-output BLADE full adder: pBW820 (Addgene: 87552)
 2-input-4-output BLADE CRISPR decoder: pBW1997 (Addgene: 87549)
 6-input-1-output Boolean LUT: pBW829 (Addgene: 87554)
Here is shown an example for the 2-input-4-output BLADE decoder circuit:
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Here is shown an example for the 3-input-2-output BLADE full adder circuit:
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PCR check/Sequencing:
Regions between UNSes can be PCR-amplified or sequenced to check if proper size
bands are present in the final assembled construct.
Ben Weinberg
U1 seq F
CATTACTCGCATCCA
U1 seq R
GAGACGAGACGAGAC
U2 seq F
GCTGGGAGTTCGTAG
U2 seq R
GCTTGGATTCTGCGT
U3 seq F
GCACTGAAGGTCCTC
U3 seq R
CGACCTTGATGTTTC
U4 seq F
CTGACCTCCTGCCAG
U4 seq R
GACTTTGCGTGTTGT
U5 seq F
GAGCCAACTCCCTTT
U5 seq R
CTCTAACGGACTTGA
U6 seq F
CTCGTTCGCTGCCAC
U6 seq R
GTATGTGACCGTAGA
U7 seq F
CAAGACGCTGGCTCT
U7 seq R
CGAGTAGTTCAGTAG
U8 seq F
CCTCGTCTCAACCAA
U8 seq R
CCAGGTGGTTGATGG
U9 seq F
GTTCCTTATCATCTG
U9 seq R
CAGTGCTCTTGTGGG
UX seq F
CCAGGATACATAGAT
UX seq R
GGTGGAAGGGCTCGG
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Recombinase Inputs:
The BLADE system utilizes tyrosine recombinases as inputs. The 2-input system uses
Cre and Flp recombinases and the 3-input system additionally utilizes VCre
recombinase.
Constitutive inputs:
 Constitutive expression of iCre by pCAG: pBW390 (Addgene: 89573)
 Constitutive expression of FlpO by pCAG: pBW391 (Addgene: 89574)
 Constitutive expression of VCreO by pCAG: pBW433 (Addgene: 89575)
Small-molecule inputs:
 4-hydroxytamoxifen-inducible Cre recombination:
o pCAG-ERT2-Cre-ERT2: (Addgene: 13777)
 Abscisic acid-inducible Flp recombination:
o pCAG-PV1-FlpO-N396-L1-ABI-NLS: pBW2286 (Addgene: 87559)
o pCAG-PV1-PYL-L1-FlpO-397C-NLS: pBW2287 (Addgene: 87560)
Compensation Controls:
We’ve included constitutively expressing fluorescent proteins that can be used for
compensation controls.
pCAG-FALSE (Addgene: 89689)
pCAG-EGFP (Addgene: 89684)
pCAG-mtagBFP (Addgene: 89685)
pCAG-mRuby2 (Addgene: 89686)
pCAG-iRFP720 (Addgene: 89687)
pCAG-LSS-mOrange (Addgene: 89688)
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Tips and Tricks:

Expression Vectors can act as Part Vectors since the AscI, NotI, and NheI of the
inserts are destroyed during the Gibson reaction and are re-introduced on the
Destination Vector backbone. Thus, one could digest assembled Part Fragments
from an Expression Vector and assemble them with additional Part Fragments in
another Gibson reaction into another Destination Vector.

An assembled Expression Vector can alternatively be extended by inserting
additional Part Fragments (via Gibson assembly) into the NotI site that precedes
the Ux sequence on the Expression Vector.
Assembly Subtleties:

Part Fragments contain 5’ sticky ends which will eventually be chewed down with
the 5’ exonuclease in the Gibson reaction; however, one (in the case of NheI) or
two nucleotide scars (AscI and NotI) will still be contained on the 3’ ends
preceding or following the UNSes. The Part Vectors have been designed
strategically to account for this. Two basepairs (GC) precede the MluI site which
homologize with the last two basepairs of the NotI site. The last two basepairs of
the Acc65I site (CC) homologize with the two basepair scar left by the AscI site.

The Destination Vectors also contain one (in the case of EcoRI) or two nucleotide
scars (NotI) while the Gibson reaction is running. Two basepairs (GC) precede the
MluI site which homologize with the last two basepairs of the NotI site and the last
basepair (C) of the NotI site on the final Part Fragment homologizes with the one
basepair scar of the EcoRI site on the Destination Vector.

The pBW series UNS vectors are not completely compatible with the pJT or pFL
series of the Silver laboratory1,2 due to the subtle base pair differences left by the
restriction enzymes. Partial interoperability may be possible using Part Fragments
made by PCR without digested restriction site sticky ends. This is less desireable
since PCR can introduce mutations, especially in priming regions due to
imperfectly synthesized oligonucleotides.

Vectors are not compatible with modular Gibson assembly systems developed by
the Weiss4 or Ellis5 laboratories.

In some cases, we had difficulties using Gibson assembly to generate guide RNAbased designs. This could be due to the short sizes of the fragments and the
similarities between each fragment. Sometimes we would see fragments missing
in the assembly. A successful alternative approach was to use overlap-extension
PCR (PCR all inserts together using a U1 forward and UX reverse primer) to fuse
the Part Fragments together and then a final Gibson assembly of the entire single
fragment into the Destination Vector.
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References:
1.
Torella, J.P. et al. Rapid construction of insulated genetic circuits via synthetic sequence-guided
isothermal assembly. Nucleic Acids Research 42, 681-689 (2014).
2.
Torella, J.P. et al. Unique nucleotide sequence-guided assembly of repetitive DNA parts for
synthetic biology applications. Nature Protocols 9, 2075-2089 (2014).
3.
Weinberg B.H. et al. Large-scale design of robust genetic circuits with multiple inputs and outputs
for mammalian cells. Nature Biotechnology (in press)
4.
Guye, P., Li, Y., Wroblewska, L., Duportet, X. & Weiss, R. Rapid, modular and reliable
construction of complex mammalian gene circuits. Nucleic acids research 41, e156 (2013).
5.
Casini, A. et al. One-pot DNA construction for synthetic biology: the Modular Overlap-Directed
Assembly with Linkers (MODAL) strategy. Nucleic acids research 42, e7 (2014).
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